Journal of Chemical Sciences

, Volume 119, Issue 5, pp 525–531 | Cite as

Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

  • Purshotam Sharma
  • Abhijit MitraEmail author
  • Sitansh Sharma
  • Harjinder Singh


The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G** level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.


Base pairing of RNA DNA sequence interaction energy of RNA RNA structures 


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Copyright information

© Indian Academy of Sciences 2007

Authors and Affiliations

  • Purshotam Sharma
    • 1
  • Abhijit Mitra
    • 1
    Email author
  • Sitansh Sharma
    • 1
  • Harjinder Singh
    • 1
  1. 1.Center for Computational Natural Sciences and BioinformaticsInternational Institute of Information TechnologyHyderabadIndia

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